By Jim Haddadin and Michelle KINGSTONjhaddadin@fosters.commkingston@fosters.com

NEWMARKET — The town has reached an agreement with the federal Environmental Protection Agency to reduce nitrogen discharge into the Great Bay watershed.

Communities around Great Bay have butted heads with the EPA during the last two years over strict new nitrogen discharge standards being phased in around the Seacoast.

Newmarket was one of five communities that filed a joint lawsuit against the state earlier this year, hoping to block new wastewater treatment regulations. Dover, Exeter, Portsmouth and Rochester are the other members of the so-called “Great Bay Municipal Coalition.”

Their lawsuit was thrown out in superior court, but as recently as last month, members of the coalition were vowing to ask the court for reconsideration in a bid to block the new standards.

However, on Monday, town officials in Newmarket released an announcement indicating the community has changed course and agreed to meet the EPA’s recommended nitrogen discharge limits, but not immediately.

“We do not agree that EPA and [the Department of Environmental Services] have addressed all of the uncertainties about the health of Great Bay,” reads an announcement released by Newmarket officials Monday. “However, we feel that it is in the best interest of our community to work with the EPA to protect Great Bay instead of entering into a lengthy and costly legal process.”

The EPA has called for Newmarket and other Great Bay communities to cap nitrogen discharge at 3 milligrams per liter. Meeting that limit will require millions of dollars worth of technological upgrades at wastewater treatment plants around the area.

Members of the Great Bay Municipal Coalition have asked the EPA to consider issuing wastewater discharge permits that cap nitrogen at 8 milligrams per liter, a level more easily attainable.

Newmarket has an antiquated wastewater treatment plant, and is already facing the prospect of designing and building a new facility, regardless of the EPA’s new nitrogen discharge limits.

Under the terms of its agreement with the EPA, Newmarket’s final permit discharge limit has been set at 3 mg/l, but the community might not ultimately be held to that standard. The EPA has granted Newmarket 15 years to achieve the new level, and an interim limit of 8.0 mg/l will be in place until then.

The agreement also incorporates an “adaptive management approach,” according to Newmarket’s announcement.

The EPA will study the nitrogen levels in Great Bay for five years after Newmarket’s new facility is operational, according to town officials. The additional monitoring period “may lead to a conclusion that the 3.0 mg/l limit is more stringent than it needs to be,” and if so, the EPA will drop the 3.0 mg/l requirement, the announcement states.

The other coalition communities, Dover, Rochester, Exeter and Portsmouth, are expecting their permits within the next two years. Newmarket’s permit is the first of 14 expired N.H. permits in the Great Bay watershed the EPA will be reissuing.

The issuance of a final permit to Newmarket came in November, following months of discussions with those concerned with the Great Bay watershed and the cost and science behind the new permits.

Newmarket Town Administrator Steve Fournier said the town is reviewing whether it will continue to participate in legal action with the Great Bay coalition.

“We still have issues with the science and want to work with our neighboring communities to address them, but we have to review what our position will be with regard to legal,” he said.

In response, the EPA called Newmarket’s decision not to appeal the EPA wastewater permit an “important step” for the health of the Lamprey River and the Great Bay watershed.

“This agreement is the result of many months of hard work by Newmarket, the regulatory agencies and other important stakeholders in the watershed to find a workable solution that meets the needs of the community and complies with the requirements of the Clean Water Act,” reads an EPA statement. “The plan for permit implementation incorporates an adaptive management approach that will allow Newmarket to make phased improvements to their sewage treatment plant, helping to reduce costs, and allow time for concurrent efforts by Newmarket and others in the Lamprey River watershed to begin to reduce other sources of nitrogen beyond the sewage treatment plant discharge.”

The final permit authorized by the EPA included alterations as a result of Newmarket’s input, according to the EPA. The agency stressed that permits are being issued to cities and towns on a case-by-case basis.

“In EPA’s view, the town’s decision to accept their permit does not create any legally or factually relevant precedent for any other[s] ... discharging in the watershed and awaiting final permits. EPA expects to issue additional permits for Great Bay dischargers in the near future,” the EPA statement reads.

Dover officials are still considering their options with regard to the nitrogen discharge issue. State Sen. David Watters, a Dover Democrat, said he hopes the Department of Environmental Services is willing to consider new scientific research about the health of Great Bay before new wastewater standards are implemented by the EPA.

“I think as the coalition communities want DES to take a look at the new scientific reports, I plan to work with DES and see if there is a way for them to re-evaluate the science,” he said. “If that is not possible, I will consider introducing legislation and get the reports to be reconsidered.”